Smoothen, close and simply surface in very complex objects
The remesh modifier will simplify your mesh and remove the smaller holes and at least some of the internal mesh. You may need to apply the modifier and then manually clean up the bigger holes.

A more manual approach is to retopologize the mesh, which is a common method used to cleanup sculpts. You can use the built-in snapping tools, the bsurfaces addon that is included with blender or CGCookies retopoflow to make it easier.